In FPcounts/FPEMglobal: Estimation of Contraceptive Use for All Women
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## set global chunk options
options(formatR.arrow=TRUE,width=80)
You can access this vignette from the R console by typing vignette("FPEMglobal_Age_1519", package = "FPEMglobal").
FPEMglobal (Family Planning Estimation Model global) implements a Bayesian hierarchical model for estimating and projecting the prevalence of contraceptive use and unmet need at the national level. This vignette concerns the application to adolescent women aged 15--19; for an introduction to the package see the vignette "FPEMglobal_Intro".
Accessing Default Input Data
Default input data for adolescent women aged 15--19 can be accessed using the system.file() command. For example:
## Find the file path in the package file tree
data_csv_filename_1519 <-
system.file("extdata", "data_cp_model_all_women_15-19.csv", #NOTE: '15-19'
package = "FPEMglobal")
## Read in the file
data_df_1519 <-
read.csv(data_csv_filename_1519, header = TRUE, as.is = TRUE)
Estimates and Projections for Adolescent Women Aged 15--19
Autopilot: All Adolescent Women Results
To implement estimation and projection for women aged 15--19 use the argument age_group = "15-19" in the functions do_global_mcmc, do_global_run, or do_global_all_women_run. The default, age_group = "15-49", will produce estimates and projections for all women of reproductive age.
Adjusted medians and special aggregates are handled in the same was as for the 15--49 age group via the arguments adjust_medians (default = FALSE) and special_aggregates_name (default = NULL), respectively.
## Do a global run for women aged 15-19, including summarization.
## Make sure you attach the package !!
library(FPEMglobal)
## Call the main function
all_women_runs_1519 <-
do_global_all_women_run(
## Describe the run
run_desc = "",
age_group = "15-19", #....................................< SELECT '15-19' HERE
data_csv_filename = "data_cp_model_all_women_15-19.csv", #< CHOOSE APPROPRIATE DATA
## MCMC parameters #......................................< CHANGE FOR FULL RUN!
estimation_iterations = 2,
burn_in_iterations = 1,
steps_before_progress_report = 1,
thinning = 1,
chain_nums = 1:2,
set_seed_chains = 1
)
## See the run name !!
## All women, married women, and unmarried women output
## folders have the same date-time in their names.
all_women_runs_1519
Age-Ratio Family Planning Indicators
FPEMglobal can produce estimates and projections of the proportion of women of reproductive age using contraceptive methods, or experiencing unment need for contraception, that are aged 15--19. These are calculated as the ratio of in the respective family planning category aged 15--19 to the number in the category aged 15--49. The calculations are done at the trajectory level yielding true probabilistic estimates.
To compute age ratio indicators a completed model run for all women of reproductive age (i.e., age 15--49) must be available for each marital group desired. The output folder(s) of these runs are referred as age_total directories. Age ratios can be requested in do_global_run or do_global_all_women_run when starting a new run, or in post_process and combine_runs when adding to an existing run. The arguments all begin with age_ratios_age_total_. See the help files ?post_process_mcmc and ?do_global_all_women_run for an explanation in each case.
do_global_all_women_run has an argument age_ratios_age_total_run_name_prefix to make it easier to select the 15--49 outputs if they follow the standard naming convention for runs explained in the vignette "FPEMglobal_Intro". All that need be supplied in that case is the common output folder name prefix. E.g.,
do_global_all_women_run(..., age_ratios_age_total_run_name_prefix = "200501_093015")
will look for the married women 15-49 outputs in "r file.path("output", FPEMglobal:::make_run_name(marital_group = "married", age_group = "15-49", run_name_override = "200501_093015"))"; unmarried and all women result output folder names will be constructed according to the same scheme.
## Do a global run for women aged 15-19, including summarization, with age ratios
# Call the main function
all_women_runs_1519 <-
do_global_all_women_run(
## Describe the run
run_desc = "",
age_group = "15-19", #....................................< SELECT '15-19' HERE
data_csv_filename = "data_cp_model_all_women_15-19.csv", #< CHOOSE APPROPRIATE DATA
## MCMC parameters #......................................< CHANGE FOR FULL RUN!
estimation_iterations = 2,
burn_in_iterations = 1,
steps_before_progress_report = 1,
thinning = 1,
chain_nums = 1:2,
set_seed_chains = 1,
## Age ratios
age_ratios_age_total_run_name_prefix = "200501_093015" #..< COMMON PREFIX OF 15-49 OUTPUT FOLDERS
)
The table below list the three methods by which the 15--49 results to be used for age ratio calculation can be selected, the functions they can be used with, and the corresponding function arguments.
+------------------------------+----------------------------------------+----------------------------------------------------------+
| Method | Function | Arguments |
+==============================+========================================+==========================================================+
| Common prefix | do_global_all_women_run | age_ratios_age_total_run_name_prefix |
+------------------------------+----------------------------------------+----------------------------------------------------------+
| Run name | do_global_run | age_ratios_age_total_run_name |
+------------------------------+----------------------------------------+----------------------------------------------------------+
| | do_global_all_women_run | age_ratios_age_total_married_run_name |
| | | age_ratios_age_total_unmarried_run_name |
| | | age_ratios_age_total_all_women_run_name |
+------------------------------+----------------------------------------+----------------------------------------------------------+
| Output folder path | do_global_run | age_ratios_age_total_output_folder_path |
+------------------------------+----------------------------------------+----------------------------------------------------------+
| | do_global_all_women_run | age_ratios_age_total_married_output_folder_path |
| | | age_ratios_age_total_unmarried_output_folder_path |
| | | age_ratios_age_total_all_women_output_folder_path |
+------------------------------+----------------------------------------+----------------------------------------------------------+
Base Level Control
Base level control is available for adding results to, or reprocessing a completed model run. See the vignette "FPEMglobal_Intro" for details. The functions post_process_mcmc, combine_runs, and make_results do not take the age_group argument; this is read from the meta information saved by the do_... functions.
In the following section, and an additional type of outputs is discussed: age ratios. The nature of this output is explained in that section. The table below gives a summary of the function call sequences needed to produce various combinations of outputs from a completed model run, including this two additional type. The completed run could have been obtained from any of the do_... functions. In the example calls, default values of arguments are assumed and are not explicitly specified. It is further assumed that the appropriate run_names are passed as the first argument to all functions.
+-----------------------+-------------------------------------------------+---------------------------------------------------------------------------------+
| Marital Group | Output | Function call sequence |
+=======================+=================================================+=================================================================================+
| Married and unmarried | Age ratios, country level | post_process_mcmc(..., age_ratios_age_total_output_folder_path = "NAME") \ |
| | | make_results |
+-----------------------+-------------------------------------------------+---------------------------------------------------------------------------------+
| | Age ratios, std. aggregates | Age ratios, country level for both marital groups and all women completed \ |
| | | make_results (must run again) |
+-----------------------+-------------------------------------------------+---------------------------------------------------------------------------------+
| | Age ratios, spec. aggregates | Age ratios, country level for both marital groups and all women completed \ |
| | | make_results(..., special_aggregates_name = "[name]") (must run again) |
+-----------------------+-------------------------------------------------+---------------------------------------------------------------------------------+
| | Adjusted median age ratios, country level | Not available |
+-----------------------+-------------------------------------------------+---------------------------------------------------------------------------------+
| | Adjusted median age ratios, std.aggregates | Not available |
+-----------------------+-------------------------------------------------+---------------------------------------------------------------------------------+
| | Adjusted median age ratios, spec. aggregates | Not available |
+-----------------------+-------------------------------------------------+---------------------------------------------------------------------------------+
| All women | Age ratios, country level | combine_runs(..., age_ratios_age_total_output_folder_path = "NAME") \ |
| | | make_results |
+-----------------------+-------------------------------------------------+---------------------------------------------------------------------------------+
| | Age ratios, std. aggregates | combine_runs(..., age_ratios_age_total_output_folder_path = "NAME") \ |
| | | make_results |
+-----------------------+-------------------------------------------------+---------------------------------------------------------------------------------+
| | Age ratios, spec. aggregates | combine_runs(..., age_ratios_age_total_output_folder_path = "NAME") \ |
| | | make_results(..., special_aggregates_name = "[name]") |
+-----------------------+-------------------------------------------------+---------------------------------------------------------------------------------+
| | Adjusted median age ratios, country level | Not available |
+-----------------------+-------------------------------------------------+---------------------------------------------------------------------------------+
| | Adjusted median age ratios, std.aggregates | Not available |
+-----------------------+-------------------------------------------------+---------------------------------------------------------------------------------+
| | Adjusted median age ratios, spec. aggregates | Not available |
+-----------------------+-------------------------------------------------+---------------------------------------------------------------------------------+
References {-}
FPcounts/FPEMglobal documentation built on July 20, 2024, 2:35 a.m.
R Package Documentation
Browse R Packages
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knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## set global chunk options options(formatR.arrow=TRUE,width=80)
You can access this vignette from the R console by typing vignette("FPEMglobal_Age_1519", package = "FPEMglobal").
FPEMglobal (Family Planning Estimation Model global) implements a Bayesian hierarchical model for estimating and projecting the prevalence of contraceptive use and unmet need at the national level. This vignette concerns the application to adolescent women aged 15--19; for an introduction to the package see the vignette "FPEMglobal_Intro".
Accessing Default Input Data
Default input data for adolescent women aged 15--19 can be accessed using the system.file() command. For example:
## Find the file path in the package file tree data_csv_filename_1519 <- system.file("extdata", "data_cp_model_all_women_15-19.csv", #NOTE: '15-19' package = "FPEMglobal") ## Read in the file data_df_1519 <- read.csv(data_csv_filename_1519, header = TRUE, as.is = TRUE)
Estimates and Projections for Adolescent Women Aged 15--19
Autopilot: All Adolescent Women Results
To implement estimation and projection for women aged 15--19 use the argument age_group = "15-19" in the functions do_global_mcmc, do_global_run, or do_global_all_women_run. The default, age_group = "15-49", will produce estimates and projections for all women of reproductive age.
Adjusted medians and special aggregates are handled in the same was as for the 15--49 age group via the arguments adjust_medians (default = FALSE) and special_aggregates_name (default = NULL), respectively.
## Do a global run for women aged 15-19, including summarization. ## Make sure you attach the package !! library(FPEMglobal) ## Call the main function all_women_runs_1519 <- do_global_all_women_run( ## Describe the run run_desc = "", age_group = "15-19", #....................................< SELECT '15-19' HERE data_csv_filename = "data_cp_model_all_women_15-19.csv", #< CHOOSE APPROPRIATE DATA ## MCMC parameters #......................................< CHANGE FOR FULL RUN! estimation_iterations = 2, burn_in_iterations = 1, steps_before_progress_report = 1, thinning = 1, chain_nums = 1:2, set_seed_chains = 1 ) ## See the run name !! ## All women, married women, and unmarried women output ## folders have the same date-time in their names. all_women_runs_1519
Age-Ratio Family Planning Indicators
FPEMglobal can produce estimates and projections of the proportion of women of reproductive age using contraceptive methods, or experiencing unment need for contraception, that are aged 15--19. These are calculated as the ratio of in the respective family planning category aged 15--19 to the number in the category aged 15--49. The calculations are done at the trajectory level yielding true probabilistic estimates.
To compute age ratio indicators a completed model run for all women of reproductive age (i.e., age 15--49) must be available for each marital group desired. The output folder(s) of these runs are referred as age_total directories. Age ratios can be requested in do_global_run or do_global_all_women_run when starting a new run, or in post_process and combine_runs when adding to an existing run. The arguments all begin with age_ratios_age_total_. See the help files ?post_process_mcmc and ?do_global_all_women_run for an explanation in each case.
do_global_all_women_run has an argument age_ratios_age_total_run_name_prefix to make it easier to select the 15--49 outputs if they follow the standard naming convention for runs explained in the vignette "FPEMglobal_Intro". All that need be supplied in that case is the common output folder name prefix. E.g.,
do_global_all_women_run(..., age_ratios_age_total_run_name_prefix = "200501_093015")
will look for the married women 15-49 outputs in "r file.path("output", FPEMglobal:::make_run_name(marital_group = "married", age_group = "15-49", run_name_override = "200501_093015"))"; unmarried and all women result output folder names will be constructed according to the same scheme.
## Do a global run for women aged 15-19, including summarization, with age ratios # Call the main function all_women_runs_1519 <- do_global_all_women_run( ## Describe the run run_desc = "", age_group = "15-19", #....................................< SELECT '15-19' HERE data_csv_filename = "data_cp_model_all_women_15-19.csv", #< CHOOSE APPROPRIATE DATA ## MCMC parameters #......................................< CHANGE FOR FULL RUN! estimation_iterations = 2, burn_in_iterations = 1, steps_before_progress_report = 1, thinning = 1, chain_nums = 1:2, set_seed_chains = 1, ## Age ratios age_ratios_age_total_run_name_prefix = "200501_093015" #..< COMMON PREFIX OF 15-49 OUTPUT FOLDERS )
The table below list the three methods by which the 15--49 results to be used for age ratio calculation can be selected, the functions they can be used with, and the corresponding function arguments.
+------------------------------+----------------------------------------+----------------------------------------------------------+
| Method | Function | Arguments |
+==============================+========================================+==========================================================+
| Common prefix | do_global_all_women_run | age_ratios_age_total_run_name_prefix |
+------------------------------+----------------------------------------+----------------------------------------------------------+
| Run name | do_global_run | age_ratios_age_total_run_name |
+------------------------------+----------------------------------------+----------------------------------------------------------+
| | do_global_all_women_run | age_ratios_age_total_married_run_name |
| | | age_ratios_age_total_unmarried_run_name |
| | | age_ratios_age_total_all_women_run_name |
+------------------------------+----------------------------------------+----------------------------------------------------------+
| Output folder path | do_global_run | age_ratios_age_total_output_folder_path |
+------------------------------+----------------------------------------+----------------------------------------------------------+
| | do_global_all_women_run | age_ratios_age_total_married_output_folder_path |
| | | age_ratios_age_total_unmarried_output_folder_path |
| | | age_ratios_age_total_all_women_output_folder_path |
+------------------------------+----------------------------------------+----------------------------------------------------------+
Base Level Control
Base level control is available for adding results to, or reprocessing a completed model run. See the vignette "FPEMglobal_Intro" for details. The functions post_process_mcmc, combine_runs, and make_results do not take the age_group argument; this is read from the meta information saved by the do_... functions.
In the following section, and an additional type of outputs is discussed: age ratios. The nature of this output is explained in that section. The table below gives a summary of the function call sequences needed to produce various combinations of outputs from a completed model run, including this two additional type. The completed run could have been obtained from any of the do_... functions. In the example calls, default values of arguments are assumed and are not explicitly specified. It is further assumed that the appropriate run_names are passed as the first argument to all functions.
+-----------------------+-------------------------------------------------+---------------------------------------------------------------------------------+
| Marital Group | Output | Function call sequence |
+=======================+=================================================+=================================================================================+
| Married and unmarried | Age ratios, country level | post_process_mcmc(..., age_ratios_age_total_output_folder_path = "NAME") \ |
| | | make_results |
+-----------------------+-------------------------------------------------+---------------------------------------------------------------------------------+
| | Age ratios, std. aggregates | Age ratios, country level for both marital groups and all women completed \ |
| | | make_results (must run again) |
+-----------------------+-------------------------------------------------+---------------------------------------------------------------------------------+
| | Age ratios, spec. aggregates | Age ratios, country level for both marital groups and all women completed \ |
| | | make_results(..., special_aggregates_name = "[name]") (must run again) |
+-----------------------+-------------------------------------------------+---------------------------------------------------------------------------------+
| | Adjusted median age ratios, country level | Not available |
+-----------------------+-------------------------------------------------+---------------------------------------------------------------------------------+
| | Adjusted median age ratios, std.aggregates | Not available |
+-----------------------+-------------------------------------------------+---------------------------------------------------------------------------------+
| | Adjusted median age ratios, spec. aggregates | Not available |
+-----------------------+-------------------------------------------------+---------------------------------------------------------------------------------+
| All women | Age ratios, country level | combine_runs(..., age_ratios_age_total_output_folder_path = "NAME") \ |
| | | make_results |
+-----------------------+-------------------------------------------------+---------------------------------------------------------------------------------+
| | Age ratios, std. aggregates | combine_runs(..., age_ratios_age_total_output_folder_path = "NAME") \ |
| | | make_results |
+-----------------------+-------------------------------------------------+---------------------------------------------------------------------------------+
| | Age ratios, spec. aggregates | combine_runs(..., age_ratios_age_total_output_folder_path = "NAME") \ |
| | | make_results(..., special_aggregates_name = "[name]") |
+-----------------------+-------------------------------------------------+---------------------------------------------------------------------------------+
| | Adjusted median age ratios, country level | Not available |
+-----------------------+-------------------------------------------------+---------------------------------------------------------------------------------+
| | Adjusted median age ratios, std.aggregates | Not available |
+-----------------------+-------------------------------------------------+---------------------------------------------------------------------------------+
| | Adjusted median age ratios, spec. aggregates | Not available |
+-----------------------+-------------------------------------------------+---------------------------------------------------------------------------------+
References {-}
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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